Quantum repeaters create long-distance entanglement between quantum systems while overcoming difficulties such as the attenuation of single photons in a fiber. Recently, an implementation of a repeater protocol based on single qubits in atomic ensembles and linear optics has been proposed [Nature 414, 413 (2001)]. Motivated by rapid experimental progress towards implementing that protocol, here we develop a more efficient scheme compatible with active purification of arbitrary errors. Using similar resources as the earlier protocol, our approach intrinsically purifies leakage out of the logical subspace and all errors within the logical subspace, leading to greatly improved performance in the presence of experimental inefficiencies. Our analysis indicates that our scheme could generate approximately one pair per 3 minutes over 1280 km distance with fidelity (F>78%) sufficient to violate Bell's inequality.